scholarly journals Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons

2011 ◽  
Vol 61 (8) ◽  
pp. 1786-1801 ◽  
Author(s):  
Rainer Borriss ◽  
Xiao-Hua Chen ◽  
Christian Rueckert ◽  
Jochen Blom ◽  
Anke Becker ◽  
...  
Keyword(s):  
16S Rrna ◽  
Dna Sequences ◽  
Bacillus Amyloliquefaciens ◽  
Type Strain ◽  
Marker Gene ◽  
Genome Comparison ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Gene Sequences ◽  
Sequence Comparisons

The whole-genome-sequenced rhizobacterium Bacillus amyloliquefaciens FZB42T (Chen et al., 2007) and other plant-associated strains of the genus Bacillus described as belonging to the species Bacillus amyloliquefaciens or Bacillus subtilis are used commercially to promote the growth and improve the health of crop plants. Previous investigations revealed that a group of strains represented a distinct ecotype related to B. amyloliquefaciens; however, the exact taxonomic position of this group remains elusive (Reva et al., 2004). In the present study, we demonstrated the ability of a group of Bacillus strains closely related to strain FZB42T to colonize Arabidopsis roots. On the basis of their phenotypic traits, the strains were similar to Bacillus amyloliquefaciens DSM 7T but differed considerably from this type strain in the DNA sequences of genes encoding 16S rRNA, gyrase subunit A (gyrA) and histidine kinase (cheA). Phylogenetic analysis performed with partial 16S rRNA, gyrA and cheA gene sequences revealed that the plant-associated strains of the genus Bacillus, including strain FZB42T, formed a lineage, which could be distinguished from the cluster of strains closely related to B. amyloliquefaciens DSM 7T. DNA–DNA hybridizations (DDH) performed with genomic DNA from strains DSM 7T and FZB42T yielded relatedness values of 63.7–71.2 %. Several methods of genomic analysis, such as direct whole-genome comparison, digital DDH and microarray-based comparative genomichybridization (M-CGH) were used as complementary tests. The group of plant-associated strains could be distinguished from strain DSM 7T and the type strain of B. subtilis by differences in the potential to synthesize non-ribosomal lipopeptides and polyketides. Based on the differences found in the marker gene sequences and the whole genomes of these strains, we propose two novel subspecies, designated B. amyloliquefaciens subsp. plantarum subsp. nov., with the type strain FZB42T ( = DSM 23117T = BGSC 10A6T), and B. amyloliquefaciens subsp. amyloliquefaciens subsp. nov., with the type strain DSM 7T( = ATCC 23350T = Fukumoto Strain FT), for plant-associated and non-plant-associated representatives, respecitvely. This is in agreement with results of DDH and M-CGH tests and the MALDI-TOF MS of cellular components, all of which suggested that the ecovars represent two different subspecies.

scholarly journals Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov.

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3344-3351 ◽  
Author(s):  
Werner Nicklas ◽  
Magne Bisgaard ◽  
Bent Aalbæk ◽  
Peter Kuhnert ◽  
Henrik Christensen
Keyword(s):  
16S Rrna ◽  
Dna Sequences ◽  
Type Strain ◽  
New Genus ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
New Combination ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Sequence Comparisons

To reinvestigate the taxonomy of [Actinobacillus] muris, 474 strains, mainly from mice and rats, were characterized by phenotype and 130 strains selected for genotypic characterization by 16S rRNA and partial rpoB gene sequencing. The type strain was further investigated by whole-genome sequencing. Phylogenetic analysis of the DNA sequences showed one monophyletic group with intragroup similarities of 96.7 and 97.2 % for the 16S rRNA and rpoB genes, respectively. The highest 16S rRNA gene sequence similarity to a taxon with a validly published name outside the group was 95.9 %, to the type strain of [Pasteurella] pneumotropica. The closest related taxon based on rpoB sequence comparison was ‘Haemophilus influenzae-murium’, with 88.4 % similarity. A new genus and a new combination, Muribacter muris gen. nov., comb. nov., are proposed based on a distinct phylogenetic position based on 16S rRNA and rpoB gene sequence comparisons, with major divergence from the existing genera of the family Pasteurellaceae. The new genus has the characteristics of [A.] muris with the emendation that acid formation from ( − )-d-mannitol and hydrolysis of aesculin are variable, while the α-glucosidase test is positive. There is no requirement for exogenously supplied NAD (V factor) for the majority of strains investigated; however, one strain was found to require NAD. The major fatty acids of the type strain of Muribacter muris were C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0, which is in line with most genera of the Pasteurellaceae. The type strain of Muribacter muris is CCUG 16938T ( = NCTC 12432T = ATCC 49577T).

scholarly journals Halalkalicoccus jeotgali sp. nov., a halophilic archaeon from shrimp jeotgal, a traditional Korean fermented seafood

2007 ◽  
Vol 57 (10) ◽  
pp. 2296-2298 ◽  
Author(s):  
Seong Woon Roh ◽  
Young-Do Nam ◽  
Ho-Won Chang ◽  
Youlboong Sung ◽  
Kyoung-Ho Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Biochemical Tests ◽  
Extremely Halophilic Archaeon ◽  
Physiological And Biochemical

A novel, extremely halophilic archaeon B3T was isolated from shrimp-salted seafood. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Strain B3T is non-motile, Gram-variable, requires at least 10 % (w/v) NaCl for growth and grows in the ranges of 21–50 °C and pH 6.5–9.0. The DNA G+C content of strain B3T was 63.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain B3T belonged to the genus Halalkalicoccus and was phylogenetically closely related to the type strain Halalkalicoccus tibetensis (98.64 %). However, DNA–DNA hybridization experiments showed 7.0 % relatedness between strain B3T and a strain of a reference species of the genus Halalkalicoccus. Combined analysis of 16S rRNA gene sequences, DNA–DNA relatedness data, physiological and biochemical tests indicated that the genotypic and phenotypic characteristics differentiate strain B3T from other Halalkalicoccus species. On the basis of the evidence presented in this report, strain B3T represents a novel species of the genus Halalkalicoccus, for which the name Halalkalicoccus jeotgali. sp. nov. is proposed. The type strain is B3T (=KCTC 4019T=DSM 18796T=JCM 14584T=CECT 7217T).

scholarly journals Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex

2011 ◽  
Vol 61 (7) ◽  
pp. 1606-1611 ◽  
Author(s):  
Enrico Tortoli ◽  
Erik C. Böttger ◽  
Anna Fabio ◽  
Enevold Falsen ◽  
Zoe Gitti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polyphasic Analysis ◽  
Mycobacterium Simiae

Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228T ( = DSM 45397T  = CCUG 58464T) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the ‘Mycobacterium simiae complex’ for this group.

Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively

2010 ◽  
Vol 60 (4) ◽  
pp. 963-971 ◽  
Author(s):  
Rafael R. de la Haba ◽  
Cristina Sánchez-Porro ◽  
M. Carmen Márquez ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The Family ◽  
23S Rrna Gene ◽  
Single Genus ◽  
Type Strains

We have carried out a polyphasic taxonomic characterization of the type strains of the species with the recently validated name Salinicola socius, together with two species that were phylogenetically closely related, Halomonas salaria and Chromohalobacter salarius. 16S rRNA gene sequence analyses showed that they constituted a coherent cluster, with sequence similarities between 98.7 and 97.7 %. We have determined the almost complete 23S rRNA gene sequences of these three type strains, and the percentage of similarity between them was 99.2–97.6 %. Phylogenetic trees based on the 16S rRNA and 23S rRNA gene sequences, obtained by using three different algorithms, were consistent and showed that these three species constituted a cluster separated from the other species of the genera of the family Halomonadaceae, supporting their placement in a single genus. All three species have ubiquinone 9 as the major respiratory quinone, and showed similar fatty acid and polar lipid profiles. The level of DNA–DNA hybridization between Salinicola socius DSM 19940T, Halomonas salaria DSM 18044T and Chromohalobacter salarius CECT 5903T was 41–21 %, indicating that they are different species of the genus Salinicola. A comparative phenotypic study of these strains following the proposed minimal standards for describing new taxa of the family Halomonadaceae has been carried out. The phenotypic data are consistent with the placement of these three species in a single genus and support their differentiation at the species level. On the basis of these data we have emended the description of the species Salinicola socius and we propose to transfer the species Halomonas salaria and Chromohalobacter salarius to the genus Salinicola, as Salinicola salarius comb. nov. (type strain M27T =KCTC 12664T =DSM 18044T) and Salinicola halophilus nom. nov. (type strain CG4.1T =CECT 5903T =LMG 23626T), respectively.

Taxonomic status of the species Clostridium methoxybenzovorans Mechichi et al. 1999

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Hisami Kobayashi ◽  
Yasuhiro Tanizawa ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
Masanori Tohno
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

The taxonomic status of the species Clostridium methoxybenzovorans was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection ( C. methoxybenzovorans ATCC 700855T) is a member of the species Eubacterium callanderi . Hence, C. methoxybenzovorans ATCC 700855T cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182T) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3T showed high sequence identity with those of Lacrimispora indolis (recently reclassified from Clostridium indolis ) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on blast and digital DNA–DNA hybridization values of 98.3 and 87.9 %, respectively. Based on these results, C. methoxybenzovorans SR3T was considered to be a member of L. indolis .

Thalassobacter stenotrophicus Macián et al. 2005 is a later synonym of Jannaschia cystaugens Adachi et al. 2004, with emended description of the genus Thalassobacter

2005 ◽  
Vol 55 (5) ◽  
pp. 1959-1963 ◽  
Author(s):  
M. J. Pujalte ◽  
M. C. Macián ◽  
D. R. Arahal ◽  
E. Garay
Keyword(s):  
16S Rrna ◽  
Genomic Dna ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Sequence Comparisons ◽  
Emended Description

The type strains of Jannaschia cystaugens (LMG 22015T) and Thalassobacter stenotrophicus (CECT 5294T) were analysed by means of genomic DNA–DNA hybridization, comparison of 16S rRNA gene sequences and phenotypic properties determined under the same methodological conditions. J. cystaugens LMG 22015T showed DNA–DNA relatedness levels of 72 % when hybridized with the genomic DNA of T. stenotrophicus CECT 5294T. Sequence comparisons revealed that the 16S rRNA genes of the two strains had a similarity of 99·8 %. The cellular fatty acid and polar lipid compositions of the two strains and their DNA mol% G+C contents were almost identical. Bacteriochlorophyll a (Bchl a) and polyhydroxybutyrate were produced by both strains under the same culture conditions. Their closest phylogenetic neighbours were Jannaschia helgolandensis and Jannaschia rubra; however, the low sequence similarity values (95·7–95·9 %) and several important differences in phenotypic traits (ionic requirements, Bchl a production and polar lipids) support the distinction between the genera Thalassobacter and Jannaschia. Thus, we propose the unification of J. cystaugens (LMG 22015T) and T. stenotrophicus (CECT 5294T) as Thalassobacter stenotrophicus (type strain, CECT 5294T=DSM 16310T). An emended description of the genus Thalassobacter is also presented.

Anaerostipes butyraticus sp. nov., an anaerobic, butyrate-producing bacterium from Clostridium cluster XIVa isolated from broiler chicken caecal content, and emended description of the genus Anaerostipes

2010 ◽  
Vol 60 (5) ◽  
pp. 1108-1112 ◽  
Author(s):  
Venessa Eeckhaut ◽  
Filip Van Immerseel ◽  
Frank Pasmans ◽  
Evie De Brandt ◽  
Freddy Haesebrouck ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Broiler Chicken ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Caecal Content ◽  
Emended Description ◽  
Bacterial Clone

Four butyrate-producing isolates were obtained from the caecal content of a 4-week-old broiler chicken. The 16S rRNA gene sequences were determined and confirmed the close relatedness of the four isolates, which suggested that they were derived from a single bacterial clone. Phylogenetic analysis based on 16S rRNA gene sequences showed that its closest relatives were members of cluster XIVa of the Clostridium subphylum of Gram-positive bacteria and that the closest related type strain was Anaerostipes caccae L1-92T (94.5 % similarity). Similarity levels of 96–98 % with sequences from uncultured bacteria from human stool samples were observed. On the basis of morphological, biochemical and phylogenetic characteristics, this strain is assigned to a novel species in the genus Anaerostipes, for which the name Anaerostipes butyraticus sp. nov. is proposed. The type strain is 35-7T (=LMG 24724T =DSM 22094T). An emended description of the genus Anaerostipes is also provided.

scholarly journals Emended description of the genus Actinokineospora Hasegawa 1988 and transfer of Amycolatopsis fastidiosa Henssen et al. 1987 as Actinokineospora fastidiosa comb. nov.

2010 ◽  
Vol 60 (6) ◽  
pp. 1444-1449 ◽  
Author(s):  
D. P. Labeda ◽  
N. P. Price ◽  
G. Y. A. Tan ◽  
M. Goodfellow ◽  
H.-P. Klenk
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Careful Evaluation ◽  
Emended Description

The species Amycolatopsis fastidiosa (ex Celmer et al. 1977) Henssen et al. 1987 was proposed, based on morphological and chemotaxonomic observations, for a strain originally described as ‘Pseudonocardia fastidiosa’ Celmer et al. 1977 in a US patent. In the course of a phylogenetic study of the taxa with validly published names within the suborder Pseudonocardineae based on 16S rRNA gene sequences, it became apparent that this species was misplaced in the genus Amycolatopsis. After careful evaluation of the phylogeny, morphology, chemotaxonomy and physiology of the type strain, it was concluded that this strain represents a species of the genus Actinokineospora that is unable to produce motile spores. The description of the genus Actinokineospora is therefore emended to accommodate species that do not produce motile spores, and it is proposed that Amycolatopsis fastidiosa be transferred to the genus Actinokineospora as Actinokineospora fastidiosa comb. nov. The type strain is NRRL B-16697T =ATCC 31181T =DSM 43855T =JCM 3276T =NBRC 14105T =VKM Ac-1419T.

scholarly journals Reclassification of Lactobacillus amylophilus LMG 11400 and NRRL B-4435 as Lactobacillus amylotrophicus sp. nov.

2006 ◽  
Vol 56 (11) ◽  
pp. 2523-2527 ◽  
Author(s):  
Sabri M. Naser ◽  
Marc Vancanneyt ◽  
Cindy Snauwaert ◽  
Gino Vrancken ◽  
Bart Hoste ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Alpha Subunit ◽  
Cell Protein ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Genes Encoding

The taxonomic position of six Lactobacillus amylophilus strains isolated from swine waste-corn fermentations was reinvestigated. All strains were included in a multilocus sequence analysis (MLSA) study for species identification of Lactobacillus using the genes encoding the phenylalanyl-tRNA synthase alpha subunit (pheS) and RNA polymerase alpha subunit (rpoA). Partial pheS and rpoA gene sequences showed that strains LMG 11400 and NRRL B-4435 represent a separate lineage that is distantly related to the type strain of L. amylophilus, LMG 6900T, and to three other strains of the species. The MLSA data showed that the two strains LMG 11400 and NRRL B-4435 constituted a distinct cluster, sharing 100 % pheS and rpoA gene sequence similarity. The other reference strains clustered together with the type strain of L. amylophilus, LMG 6900T, and were clearly differentiated from strains LMG 11400 and NRRL B-4435 (80 and 89 % pheS and rpoA gene sequence similarity, respectively). The 16S rRNA gene sequences of the latter two strains are 100 % identical, with the nearest phylogenetic neighbour L. amylophilus LMG 6900T showing only 97.2 % 16S rRNA gene sequence similarity. Further polyphasic taxonomic study based on whole-cell protein fingerprinting, DNA–DNA hybridization and biochemical features demonstrated that the two strains represent a single, novel Lactobacillus species, for which the name Lactobacillus amylotrophicus sp. nov. is proposed. The type strain is LMG 11400T (=NRRL B-4436T=DSM 20534T).

scholarly journals Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.

2005 ◽  
Vol 55 (1) ◽  
pp. 153-157 ◽  
Author(s):  
Valme Jurado ◽  
Ingrid Groth ◽  
Juan M. Gonzalez ◽  
Leonila Laiz ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA–DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces neolithicus sp. nov. (type strain, 23-23T=HKI 0321T=DSM 16197T=NCIMB 13989T).

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